FluView Wk 52: A Slight Increase In Activity & A Novel H3N2v In New Jersey

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Influenza activity remains fairly low for this time of year, but has increased slightly in recent weeks. Interestingly, a flu season that early on appeared destined to be dominated by H3N2 has - in the past month - switched over to seeing a majority of H1N1 cases.

Today's FluView also carries a report on the 7th novel swine variant flu infection of the year.

First a quick look at the regular flu stats, then a look at the novel flu detection.

2015-2016 Influenza Season Week 52 ending January 2, 2016

All data are preliminary and may change as more reports are received.

Synopsis:

During week 52 (December 26, 2015-January 2, 2016), influenza activity increased slightly in the United States.

• Viral Surveillance: The most frequently identified influenza virus type reported by public health laboratories during week 52 was influenza A, with influenza A (H1N1)pdm09 viruses predominating. The percentage of respiratory specimens testing positive for influenza in clinical laboratories was low.
• Novel Influenza A Virus: One human infection with a novel influenza A virus was reported.
• Pneumonia and Influenza Mortality: The proportion of deaths attributed to pneumonia and influenza (P&I) was below their system-specific epidemic threshold in both the NCHS Mortality Surveillance System and the 122 Cities Mortality Reporting System.
• Influenza-associated Pediatric Deaths: Two influenza-associated pediatric deaths were reported.
• Outpatient Illness Surveillance: The proportion of outpatient visits for influenza-like illness (ILI) was 2.8%, which is above the national baseline of 2.1%. Seven of 10 regions reported ILI at or above region-specific baseline levels. Puerto Rico and two states experienced high ILI activity; New York City and two states experienced moderate ILI activity; seven states experienced low ILI activity; 39 states experienced minimal ILI activity; and the District of Columbia had insufficient data.
• Geographic Spread of Influenza: The geographic spread of influenza in Guam and two states were reported as widespread; six states reported regional activity; 13 states reported local activity; the U.S. Virgin Islands and 27 states reported sporadic activity; the District of Columbia and two states reported no influenza activity; and Puerto Rico did not report.

      
           (Continue . . . )

 
While only rarely reported – partly due to limited surveillance and testing – swine variant influenza infections are suspected to be more common than we know (see CID Journal: Estimates Of Human Infection From H3N2v (Jul 2011-Apr 2012).

 Illness due to these strains is usually mild to moderate, and the symptoms look like any other flu.

Up until about six years ago the CDC only received 1 or 2 swine variant infection reports each year. In 2010, that number jumped to 8, and in 2011 to 12. In 2012 we saw more than 300 cases – mostly mild - and nearly all associated with exposure to pigs at state and local agricultural fairs.

In 2015 we've received word of 7 cases (4 - H1N1v & 3 - H3N2v).   Today's FluView has the details on this latest detection, which comes from New Jersey.

Novel Influenza A Virus:

One human infection with a novel influenza A virus was reported by the state of New Jersey. The person was infected with an influenza A (H3N2) variant (H3N2v) virus. The patient was not hospitalized and has fully recovered from their illness. The patient visited a farm near where swine are frequently housed but no direct contact with swine was reported in the week prior to illness onset. No ongoing human-to-human transmission has been identified.

Early identification and investigation of human infections with novel influenza A viruses are critical so that the risk of infection can be more fully appreciated and appropriate public health measures can be taken. Additional information on influenza in swine, variant influenza infection in humans, and strategies to interact safely with swine can be found at http://www.cdc.gov/flu/swineflu/index.htm.

While we’ve not seen sustained or efficient spread of these swine variant viruses in humans - like all flu viruses - swine variant viruses are capable of evolving, reassorting, and adapting to their hosts. Last summer we looked at a study that examine two recently discovered swine variant strains (see J. Virol: Novel Reassortant Human-like H3N2 & H3N1 Influenza A Viruses In Pigs).
 

They described both of these novel subtypes as “. . . virulent and can sustain onward transmission in pigs, and the naturally occurring mutations in the HA were associated with antigenic divergence from H3 IAV from human and swine’” and goes on to warn that  ``. . . the potential risk of these emerging swine IAV to humans should be considered”.

 
Although avian flu gets most of the headlines – mostly due to their high fatality rate – swine flu viruses are considered more likely to jump to humans, simply because they fall in the same H1, H2, and H3 subtypes as `humanized’ flu strains of the past 130 years.   
 

The 2009 H1N1 pandemic virus evolved in pigs, and so easily could the next pandemic virus.

 
For some more recent blogs on swine and swine variant influenza, you may wish to revisit:

 

PNAS: The Pandemic Potential Of Eurasian Avian-like H1N1 (EAH1N1) Swine Influenza

Eurosurveillance: Seroprevalence Of Cross-Reactive Antibodies To Swine H3N2v – Germany
 
JID: Evolutionary Dynamics Of Influenza A Viruses In US Exhibition Swine

 
Live Markets & Novel Flu Risks In The United States

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Referral: McKenna On The Latest MCR-1 Findings

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Although I've written on the recently announced MCR-1 colistin-resistance gene several times over the past couple of months (see The Lancet: Dissemination Of The MCR-1 Colistin Resistance Gene  &  Return of the Plasmids), the real `go to' person on all things antibiotic resistant is journalist, author, and blogger Maryn McKenna.

Maryn is not only the author of the award winning SUPERBUG: The Fatal Menace of MRSA, she has spent more time blogging on these issues than anyone I know. 

Late yesterday The Lancet published several new letters on recent MCR-1 findings around the globe, and Maryn has the analysis.  Follow the link to read:

Germination

A Blog by Maryn McKenna

Last-Ditch Resistance: More Countries, More Dire Results

Posted Thu, 01/7/2016

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The `M' Word

 


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If you want to draw your reader's attention to an infectious disease story, including the `M' word - `Mutation' - in the headline is a surefire technique. For most people, the `M' word evokes a sense of dread - a belief that something `bad' has happened.

A concept, I suspect, that has been fostered by scores of grade-B Sci-Fi movies over the past 60 years that always seem to use `mutations' as the genesis of their `monsters'. 

The truth is, viruses are constantly mutating.  It's what they do.  It's part of the evolutionary process.  RNA viruses - like influenza and MERS - are particularly prone to `duplication errors' during replication, and are constantly introducing mutations.


Most are of little consequence, and do nothing to affect transmissibility, replication, host range, or virulence. Some prove detrimental, making the virus less `fit' than its predecessors, and they end up as evolutionary failures. 

Only rarely does a mutation enhance a virus in a way to make it deadlier, more transmissible, or a greater threat. 

That isn't to say it doesn't ever happen.   A few examples include:

• A mutation in the envelope protein gene (E1-A226V) of the CHKV virus allowed Aedes Albopictus or `Asian tiger’ mosquito to transmit the virus more efficiently (see A Single Mutation in Chikungunya Virus Affects Vector Specificity and Epidemic Potential).
• The H275Y mutation in seasonal H1N1 back in 2007-2008 pretty much negated the effectiveness of NAI (Neuraminidase Inhibiting) antiviral drugs (see CIDRAP article With H1N1 resistance, CDC changes advice on flu drugs). Luckily that virus was supplanted by the 2009 H1N1 virus, which remains susceptible the drug.
• And for avian flu, researchers have determined the (E627K) substitution in the (PB2) protein makes the an influenza virus better able to replicate at the lower temperatures (roughly 33C) normally found in the upper human respiratory tract (see Eurosurveillance: Genetic Analysis Of Novel H7N9 Virus).

But when a new mutation is observed, scientists rarely know immediately what effects it will have on a virus. Determining that can take months of observation and research.   Complicating matters, mutations don't happen in a vacuum.

Changes often occur in multiple regions of the virus simultaneously, and different combinations may yield different outcomes.

Last summer, during the height of Korea's MERS outbreak, initial reports stated that the Korean MERS Sequences Closely Match Middle Eastern Virus. `Closely' isn't the same as `exactly', of course, and figuring out what - if any - impact minor changes might have isn't easy.


Overnight the Korean and International press is filled with reports announcing a `mutation' in the Korean MERS strain, and that it may have contributed to the virus's rapid spread.

Mutation found in MERS virus in Korea

By Kim Se-jeong

The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) which swept Korea last year underwent a mutation not found in the strains of MERs samples collected in Saudi Arabia, according to the Korea Centers for Disease Control and Prevention (KCDC), Friday.

The mutation may have affected the virulence of the virus as it has shown different patterns of spreading and infection in Korea from those in Saudi Arabia, such as an unusually fast human-to-human transmission.

While investigators suspected a mutation at the time of the epidemic, health authorities denied it.

This is the first official confirmation of the mutation.

(Continue . . . )

Showing some restraint, this article only used the word `mutation' 7 times (counting the headline).   Sparking all this ballyhoo is a dispatch, appearing in the EID journal, which finds:

Volume 22, Number 1—January 2016

Dispatch

Variations in Spike Glycoprotein Gene of MERS-CoV, South Korea, 2015

Dae-Won Kim¹, You-Jin Kim¹, Sung Han Park, Mi-Ran Yun, Jeong-Sun Yang, Hae Ji Kang, Young Woo Han, Han Saem Lee, Heui Man Kim, Hak Kim, A-Reum Kim, Deok Rim Heo, Su Jin Kim, Jun Ho Jeon, Deokbum Park, Joo Ae Kim, Hyang-Min Cheong, Jeong-Gu Nam, Kisoon Kim, and Sung Soon Kim 

Author affiliations: Korea Centers for Disease Control and Prevention, Cheongju-si, South Korea

Suggested citation for this article

Abstract

An outbreak of nosocomial infections with Middle East respiratory syndrome coronavirus occurred in South Korea in May 2015. Spike glycoprotein genes of virus strains from South Korea were closely related to those of strains from Riyadh, Saudi Arabia. However, virus strains from South Korea showed strain-specific variations.

(SNIP)

Conclusions

Accurate genome sequencing can identify spatiotemporal patterns that help understand dynamics of rapid spread of MERS-CoV infection. We report S glycoprotein gene sequences of MERS-CoV from 8 patients and a strain cultured in Vero cells. Genetic information obtained is useful for understanding the evolutionary history of MERS-CoV.

On the basis of our phylogenetic analyses, virus sequences of strains isolated in South Korea in 2015 form a unique clade. Genetic variations elucidated in this study show an unreported sequence in the RBD, which suggests that MERS-CoV circulating in South Korea during the outbreak in 2015 has higher genetic variability and mutation rates. However, we cannot conclude that deleterious effects promoting spread of infection will occur because of these mutations. Additional genetic information will resolve precise characteristics of the MERS-CoV obtained during the outbreak in South Korea.

(Continue . . .)

In other words, researchers found enough genetic variance among the small subset of the Korean viruses they sequenced to place them into a new clade. Two mutations were in the receptor binding domain of the virus's spike protein.

Interesting, but their significance is far from clear. 

To determine that may take months, or even years. By the time we know what they mean, additional changes to the virus may have rendered the point moot. Or not.  We'll see.

But at least for now, the ability to invoke the  `M' word in headlines will probably sell a lot of newspapers. 

Dr. Ian Mackay on his VDU blog this morning goes into more detail on Korean MERS research, and these reported changes to the virus.  Follow the link below to read:

Research on MERS in South Korea seems fractured...

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RESEP PUDING SUSU JAGUNG ENAK LEMBUT

Resep Puding Susu Jagung Enak dan Lembut - Puding susu sederhana yang terbuat dari kombinasi jagung manis ini merupakan variasi puding jagung tanpa santan yang sangat enak dan lembut. Puding susu segar yang lembut sehingga lumer di mulut, terbukti sangat digemari mulai dari anak-anak hingga lansia. Cita rasanya yang enak dan lezat sangat menjanjikan untuk dijadikan sebagai menu dessert favorit keluarga.

Proses cara membuat puding susu jagung cukup mudah dan praktis, serta hanya menggunakan bahan-bahan yang sederhana. Seperti halnya susu cair, bisa menggunakan susu kental manis atau susu bubuk yang dicairkan atau memakai susu cair kemasan, bahkan susu murni segar hingga susu kedelai pun dapat dijadikan pilihan.

Persiapan Bahan Puding Susu Jagung

• 1 bungkus agar-agar putih
• 800 ml susu cair
• 2 buah jagung manis
• 100 gram gula pasir
• 1/2 sdt garam
• 20 gram tepung maizena dilarutkan dengan 4 sdm susu cair
• pewarna kuning sesuai selera

Cara Membuat Puding Susu Jagung

1. Rebus jagung manis hingga matang, angkat dan tiriskan, lalu pipil jagungnya setelah cukup dingin. Blender pipilan jagung bersama susu cair hingga halus, kemudian saring.
2. Setelah disaring, campurkan dengan agar-agar putih, gula pasir dan garam dalam sebuah panci. Aduk-aduk rata hingga tidak ada yang menggumpal, tambahkan pewarna makanan sesuai selera serta aduk rata.
3. Masak adonan tadi sambil terus diaduk hingga mendidih, masukkan larutan maizena serta terus diaduk sampai adonan mengental dan tercampur rata serta mendidih kembali.
4. Angkat dan tuang dalam cetakan, karena tekstur puding yang lembut, sebaiknya gunakan cetakan kecil saja atau cup/gelas. Dinginkan dalam kulkas hingga mengeras lalu siap untuk disajikan.

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WHO MERS Update - Oman

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Earlier this week in Oman: MOH Announces 7th MERS Case, we learned of a new Coronavirus infection, but few details were provided. Today the World Health Organization has posted an update which provides the onset dates (Dec 25th), hospitalization date (Jan 1st), and possible exposure (camels) on this 44 year old male patient. 

Middle East respiratory syndrome coronavirus (MERS-CoV) – Oman

Disease outbreak news
7 January 2016

 
On 3 January 2016, the National IHR Focal Point of Oman notified WHO of 1 additional case of Middle East respiratory syndrome coronavirus (MERS-CoV) infection.

Details of the case

A 44-year-old male from the North Batinah Governorate developed symptoms on 25 December and, on 1 January, was admitted to hospital. On 3 January, the patient, who has no comorbidities, tested positive for MERS-CoV. Currently, he is in stable condition in a negative pressure isolation room on a ward. The patient has a history of exposure to dromedary camels in the 14 days prior to the onset of symptoms. He has no history of exposure to other known risk factors in the 14 days prior to the onset of symptoms. Contact tracing of household contacts is ongoing for the case. Investigation of camels is also ongoing.

Globally, since September 2012, WHO has been notified of 1,626 laboratory-confirmed cases of infection with MERS-CoV, including at least 586 related deaths.

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French MOA: 67th HPAI Outbreak Across 7 Departments

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Although the number of new outbreaks continues at a much reduced rate over last month, the French MOA continues to identify sporadic new HPAI outbreaks across the nation's southwest.  

While the impacts have been relatively small, they involve five new strains of avian flu, all said to be of `European lineage', and not descended from the more dangerous Asian H5N1 virus.

Details on these viruses (HPAI H5N1, H5N2, H5N9 and LPAI H5N2, H5N3), and how they all emerged more or less simultaneously in France, have been slow to emerge.  The last DEFRA Update On France's HPAI Outbreak (Dec 24th) cited this lack of information as hampering their ability to produce a full threats analysis.

The most recent outbreak comes from the Pyrénées Atlantiques, and is the first reported there since December 20th.

- An outbreak was declared on Jan. 6, 2016 on a farm of 10,000 chickens and 4,000 ducks in the town of Gabat

Here is the latest (translated) update from the French MOA. 

What is the current situation in France? (updated on 01/07/2016 at 15h)

In total, to date, 67 of highly pathogenic avian influenza outbreaks in poultry were detected in 7 southwestern departments of France.

ANSES gave its opinion delivered on 14 December 2015, on the potential danger to humans from the avian influenza strain identified, including the results of the complete sequencing of the H5N1 strain detected in the first home in the Dordogne. She confirmed the absence for this dangerous H5N1 strain of the key markers for human.

Find below the details of homes by department below:

In the Dordogne, 13 homes

In the Landes, 28 homes

In Haute-Vienne, a home

In Gers, 10 homes

In the Pyrénées Atlantiques, 11 homes

In the Hautes-Pyrénées, 3 fireplaces

In the Lot: a home

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HK CHP: 3rd H5N6 Case In Guangdong Province In Last 2 Weeks

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The H5N6 virus was first reported 20 months ago in Southern China, and during the first 19 months China reported a total of four human infections.  While the virus has been sporadically reported in poultry in both Vietnam and Laos, no human infections have been reported outside of China.

Two weeks ago, Guangdong Province reported a human infection (see Hong Kong Notification: Fatal H7N9 Case In Guangdong Province), followed just last week with Guangdong Province Reports 2nd H5N6 Case In A Week. 

Today Hong Kong's CHP is reporting a 3rd case in neighboring Guangdong Province.  While three cases does not an epidemic make, this sudden increase in reported cases is certainly something to watch.

CHP notified of additional human case of avian influenza A(H5N6) in Guangdong

 
The Centre for Health Protection (CHP) of the Department of Health (DH) was notified of an additional human case of avian influenza A (H5N6) by the Health and Family Planning Commission of Guangdong Province today (January 7), and again urged the public to maintain strict personal, food and environmental hygiene both locally and during travel.

It involves a man aged 25 in Longgang, Shenzhen, currently hospitalised for treatment in serious condition.?

From 2014 to date, a total of seven human cases of avian influenza A(H5N6) have been reported by the Mainland health authorities.

(Continue . . .)

It is worth noting that a couple of days ago Hong Kong announced H5N6 Detected In Dead Egret, making the 4th such detection in wild or migratory birds in the new territories.

H5N6 is one of the new reassortant viruses to come out of China since 2013, a list that includes H7N9, H5N8 (and its reassortants), and H5N6.

Of these, H7N9 has infected the most humans (roughly 700), while H5N8 - which has not infected humans - has spread the furthest afield (making it to Europe, Taiwan, Japan, and North America). 


Of these three, H5N6 is the biggest unknown, having been studied the least.  That, of course, could start to change if this virus begins to pose a serious public health threat.  For some previous studies, you may wish to revisit:

FAO-EMPRES Report On The Emergence And Threat Of H5N6

H5N6 Rising: Infecting Birds, Humans, & Even Cats

EID Journal: Influenza A(H5N6) Virus Reassortant, Southern China, 2014

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